Description

Nebularine (purine riboside) lacks exocyclic
functional groups and offers an altered hydrogen
bonding scheme while retaining base stacking
ability.1-4 It can be viewed as an
adenosine analog with the hydrogen bond donor
deleted. Sequential replacement of conserved
adenosine residues in hammerhead ribozymes by
nebularine residues2b,3 suggested the
presence of interstrand non-Watson-Crick hydrogen
bonding.2b Depending on the position of
the nebularine residue, cleavage rates were
either unchanged or diminished.2b,3
Incorporation of nebularine into a GNRA tetraloop
has also been useful for studying this type of
RNA structural feature.4 Nebularine has
been installed into RNA using two different
phosphoramidites, one with 2'-O-THP
protection1 and one with
2'-O-TBDMS protection.2-4 We
offer the latter, Nebularine CEP (BA 0265,
download Product
Information) as well as the 2-deoxy version,
2'-Deoxynebularine
CEP (BA 0016).

Description

Deletion of the O6 carbonyl group of guanosine
results in 2-aminopurine riboside (2-AP). The
hydrogen bonding pattern of the 2-aminopurine
nucleobase (N1 acceptor, H-N2 donor) is isomeric
with that of adenosine (N1 acceptor, H-N6 donor).
This nucleoside allows the study of the role of
exocyclic functional groups, base stacking, and
hydrogen bonding patterns in purine-containing
nucleic acids. For example, replacement of
guanosine residues with 2-AP in the core region
of hammerhead ribozymes was useful in determining
their role in stabilizing the transition state of
ribozyme cleavage.1 The nature of
hydrogen-bonding between G-A mismatches in RNA
internal loops was studied with 2-AP.2
The role of hydrogen-bonding and stacking
interactions in the stability of GNRA loops was
probed using 2-AP substitutions.3 The
thermodynamic parameters for RNA loops of the
type (A)n were determined using
time-resolved spectrofluorimetry on RNAs bearing
2-AP residues in place of A residues, since 2-AP
is blue fluorescent and was found to have
properties in the (A)n region that
were otherwise very similar to
adenosine.4 In this sense, 2-AP can be
used as a non-invasive conformational probe in
RNA studies. Of the different phosphoramidites
that have been used for 2-aminopurine riboside
incorporation into RNA
oligonucleotides,1-5 we have chosen to
offer 2-Aminopurine riboside CEP in the
particular form shown,1,4 which
appears to offer the best results in RNA
synthesis yield and purity. Download Product Information.

Description

The 2'-deoxyribonucleoside phosphoramidite 8-Aza-7-deaza-dA CEP, also known as PPA CEP, features a nucleobase that is isosteric with adenine but offers a different pi-electron distribution and thus an altered dipole moment, resulting in stronger stacking interactions in oligonucleotides.1 We now offer the ribonucleoside version, 8-Aza-7-deaza-A CEP (PPA Riboside CEP, BA 0267), a new compound, for use in the synthesis of altered RNA oligonucleotides.

(1) Seela, F.; Kaiser, K. Helv. Chim. Acta1988, 71, 1813-1823. Seela describes the N6-benzoyl version of the phosphoramidite of 2'-deoxy-8-aza-7-deaza-A. The N-(dimethylamino)methylidene version of the 2'-deoxy version is available from Berry & Associates (BA 0239) or from Glen Research (#1083).

Notes

8-Aza-7-deaza-a CEP features a nucleobase that is isosteric with adenine but offers a different pi-electron distribution.

Alternate Name(s):

Description

The N7 imidazole nitrogen of purine nucleosides is known to take part in
non-Watson-Crick hydrogen bonding and in metal chelation. "Deleting" the N7
nitrogen by replacing it with a CH group is a useful modification that has been
accomplished in DNA and RNA oligonucleotides using the phosphoramidites of
7-deaza-dA (2'-deoxytubercidin) and 7-deaza-A (tubercidin), respectively. Early
work by Seela1 involved 7-Deaza-dA
CEP (BA 0001),
which was useful in showing
that N7 of dA is an important hydrogen bond
acceptor site for the endodeoxyribonuclease
Eco RI. For RNA work,
we offer 7-Deaza-A CEP (BA 0268), also known
as Tubercidin CEP or C7A CEP. This
phosphoramidite has been used for studies of the
role of the N7 adenosine nitrogen in the
structure and function of tRNA and
ribozymes.2,3 Download a a Product Information
sheet for more information.